Father Figure
by Rboooks
Summary: Everyone knew Superman had a problem with his clone which was why he refused to be the father Superboy needed. The responsibly is picked up by another Cadmus experiment who is annoying, hears a voice in his head, and lives to cause the Justice league a head ache. To stay close to his son the man becomes a hero even if he is a little insane, Superboy couldn't ask for a better dad.
1. Chapter 1

**Hi everyone, thank you for giving this fic a chance! This is my first ever Naruto and Young justice crossover! I have recently been pulled back into the young justice fandom because of my OTP bluepluse! Now this fic does not have those two (sadly) but after reading some great fanfics, for the YJ fandom, I thought of my lovable Naruto, then thought "why not both?" thus I got this idea and just had to write it! It's really more of a idea and I don't know if I will finfish it but if you like it I just might! Anyway enough about that, here is chapter 1! Hope you enjoy!**

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"Take a deep breath. In. Out. In. Out. Better?" = talking

 _W-what-? where did he go! = thinking/ mental link_

 **"You are strong true, but you lack balance young kit" = Kurama talking / zeta beams**

 ** _Kit has been growing too attached... = Kurama thinking_**

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Chapter 1

Project Kr felt the moment his holding room door was opened. It wasn't a dramatic change, not even by a little, but it was there. In the tiny extra amount of noise that his super hearing could pick up as the door slid opened, in the chemical aromas that clung to the scientists as they walked in and in the way the light change oh so slightly, to be a bit brighter so said scientists could see. He felt them move around like annoying buzzing bees , as they dragged something heavy in after them , and placed it somewhere near his pod. He steeled himself in case it was a new machine they needed to use for experimenting or testing his abilities, most often than not leaving him sore and in pain. They didn't go near him or even type away on the keyboard of his pod however -much to his relief- instead barked out orders to one another as they began with the "new experiment" whatever that was.

Still if it meant that they wouldn't put him through new painful tests, Project Kr wasn't complaining for the lack of attention. It was one of the reasons he pretended to be in an unconscious-like stage whenever his creators came for a visit. Most of the scientists that came to his little home treated him like a thing instead of a person, staring at him like one would a computer or a little bug trapped in jar for study. They weren't wrong but it still stung when they acted as if he couldn't understand a single word they said. Those that knew he _could,_ however, were far worse as they seem to enjoy reminding Project Kr that he wasn't more than their weapon, their creation, their slave.

It was his own personal torture. And they knew that.

If the subject was asleep however then there would be no point in tormenting it. So hence he sleep, or _seem_ to be at least. He knew how to even out his breaths to make them barely noticeable, knew how to keep his face relax almost blank and always made sure to exaggerate his movement whenever someone opened his pod to create the illusion of him barely waking from a long slumber. He never forgot to flexed his hands before tightening them as if though his muscles were stiff from lack of use to really sell the act too.

The best part of all was that his creators always bought it. It made him feel just the slightest bit rebellious in his own secret way, which gave him a sense of his own person. He liked to pretend that he was a rebellious teenager like everyone else who had been born normal and lived a normal life of sneaking out of the house, then slipping back in when his parents checked up on him believing he had been fast asleep in his room the whole night all the while not knowing he had gone to a high school party with his friends.

It was a nice fantasy that he allowed himself to think about when he started his act.

The loud bang followed by cursing ripped him out of the slow dance with an imaginary girl he had made up for the scenario " My girlfriend is more important than the grounding my parents gave me" . He hadn't even given her a name yet, but he felt it would be Roxy. Perhaps it was because he imagined her with red hair...though now he would never be able to continue that dance. His pretend life were like dreams; you could remember bits and pieces of it but never have the same dream twice.

Mentally sighing he blamed the scientists that were thrown in a frenzying about the experiment becoming unstable. Apparently from what he could gather without revealing the fact he was awake, was that one of the rookies accidently got too close to the machine and the greenie had somehow almost gotten hurt because of it. Instead of being logical, the man had let go of whatever he was helping hold and the others had not been able to keep it up due to its weight hence the loud bang and curses from the others.

Project Kr wondered why they hadn't just make him do all the heavy lifting, it was after all one of his best features. He could have helped them get it done a lot faster than the stumbling effort they all seemed to be doing so why haven't they asked or at least ordered him to do it? He answered his own question as soon as it entered his mind leaving a bitter taste in his mouth.

 _"You're nothing but a weapon. You weren't even brought to this world by birth, no you were **grown.** What makes you think we would need help from something like you? _ The words of his creator Doctor Desmond came back to haunt him, falling onto his ears as if the doctor himself whispered them in that moment even though it had been a few weeks prior. He could still hear the mock and disgust in each word as the head scientist turned up his nose when his latest _experiment_ had offered to assist in a similar situation. It had hurt more than the sock levels of sixteen- the highest he could go before it become unbearable- that the man forced him to undergo later that day because that pain left after a few hours, the words however, still stung to this day.

Deciding he didn't want to live through _that_ again Project Kr remained silent listening to the struggles of the stress workers in front of him, hoping they would leave soon. After a few moments of them talking and setting up whatever it was, they left as quickly as they came sounding oddly tired but satisfied. He waited a few minutes just to be sure they would not be returning before relaxing back into his fantasy once more. Maybe this time he could think of something for the scenario "I got an F in Algebra so I better enjoy tonight. Mom and Dad are going to murder me tomorrow anyway".

Project Kr imaged himself sitting on the school stairs with a group of close friends on a Friday afternoon, a tight expression on his face as he scanned his report card. He would be a straight A student had it not been for that cursed Algebra test two days before grades locked. It was seventy percent of his final grade too! How unfair was that? When his father found out about this then Jr. - his name, his real _normal_ name not Kr but _J_ r- could kiss his ass goodbye-

"Hey!" A soft voice called out to him starting him from his day dream. There was someone still in the room? How!? He was sure he was alone! "Hey kid! You alright? How long have you been in here? Are you in pain?"

Odd. The Cadmus workers never cared if their experiments caused pain. They only cared about results, about how well their invention followed orders or filled expectations. They had never asked if he was okay or ever wondered how long he had been in his pod. They knew. They made him after all. Project Kr was nothing more than that to them: a project. A weapon. Not something capable of pain. Not something that could give an opinion. And defiantly not a _kid._

He is a clone, made from stolen DNA of the Man of Steel himself, Earths mightiest hero and Cadmus greatest enemy: Superman. His only reason for existing is to one day replace the original. To one day kill him in battle then slip into his life as if there had never been a clone to begin with, earn the trust of the rest of the justice league and serve the world on a silver platter to the Cadmus leaders once he got rid of each member one by one. Project Kr know this from the day he could have conscious thought without the help of the genomorph in charge of force feeding him knowledge via printed images into his mind. He knew he was a cheap copy. Knew that one day if Cadmus demand it, he would be killed without a second thought. There was no other choice in life, not for him.

He knew all of this, didn't mean he liked it. Didn't mean he would give them the satisfaction of knowing how much it scared him.

He remind still refusing to reply to the voice least they notice how irritated he felt about his existence, hoping the scientist that had stay would grow bored or believe he was in the middle of another "lesson". Even from inside the pod he called home the clone could clearly hear the insulted snort "You know kid if you're going to be a wannabe Uchiha and act as if I don't exist then at least have the decency to be good at acting!"

The air in his lungs froze. He felt a cold sweat break all over his body. No. They couldn't have found him out. They couldn't have realized his only guilty pleasure. They would take it away. They would take away his only happiness. _No!_ But no amount of hoping could keep him from realizing the truth, _they knew._ If they knew about his "sleeping" did it mean they knew about his dark secret of wanting to escape? Did they know he wanted to go meet Superman and work alongside the man instead of replacing him? Did they know all the horrible disobedient things he called the scientist in the privacy of his mind?

If they did then they would be angry. And if they were angry then it meant he would be in pain, _if he was lucky_. Who is to say they wouldn't scraped him right there and then? Who is to say they couldn't make _more_ clones? Why would they keep him around if they could? They wouldn't and that made it even harder to breathe. It took him a whale to understand why though , a small part of him checking off the symptoms from the list of human behavior that the genomorphs placed in his head as he did so .

He was terrified.

Project Kr's eyes snapped open, ready to give a explanation for his stupid behavior. He needed to make them understand why he had done what he done. To make them see that he just wanted be left alone to his thoughts because then he could focus on his duty to them, and that he defiantly _not_ trying to escape into his own mind. He just wanted to feel normal for a few hours, completely harmless. It wasn't like he ever actually followed through on those small desires anyway. Surely there was a way he could phase his words to make it sound less like a excuse? Because that was what he felt wanted to come out of his mouth in that panic moment. _There had to be!_

He forced himself not to blink the moment his eyes could stand the light least they take it as a sign of weakness. After leaving being the dark for so long it was always hard for the clone to adjust to the amount brightest around him. But right now wasn't about the slight uncomforted of his pupils, it was about looking useful and not getting thrown out as a fail experiment. Mind racing a million miles per second Project Kr already had his mouth even before his eyes were, ready to sound as persuasive as possible to accomplish just that when his eyes took survey of the room. Whatever excuse he had died in his throat before it even made it out. The young clone didn't know what he had expected to see when he opened his eyes, but it wasn't this.

The first thing he noticed was the change to his room. While he had never took one step outside his pod he had spent hours upon hours studying the little room he was created in if only to relive his boredom. He had always wondered why they were large unused wires coming out of the walls adjust to him when they served no purpose. If there was one thing he knew about Cadmus was that if it was in the lab it was there for a useful reason and if it wasn't there it is was because Cadmus didn't need it. Simple as that. So he always wondered why those wires were there when they obviously did nothing at all.

The giant pod hook up to the wall now gave him his answer. It was large in size but not so much in height and it looked more like a cell in design then a containment unit meant to hold whatever experiment the scientist thought up of. The pod was equipped with chains, a torturing looking table, nasty looking locks, heavy metal that he knew he wouldn't able to lift and the wires from the wall formed a large electric force field surrounding it. The glass that made up the walls of the pod -which the clone knew was bullet proof and super human proof- allowed him to look into the interior made it clear that it was meant to hold a strong prisoner.

And said prisoner was staring right back at him. Which happen to be the second thing he notice, and that was blue.

The most beautiful blue he had ever seen, including the mental images imprinted into his head of the world, captivated him because it was a shade he didn't even know existed. They were eyes, the clone realized, as they seem to dance with mischief and cheer. Project Kr could practically feel the child-like prankster the other was as he and the prisoner locked gazes. He then noticed the tan face they belong to. There were laugh lines that Project Kr had never seen in real life, and they pulled around the eyes and mouth of the other almost too easily. Sun kissed hair, nearly gold, spiked in all directions sat on top of the prisoner's head. But what really got his attention was the three even lines on each of the prisoner's checks, too precise to be accidental, (maybe birth marks?) and they resemble whiskers found on cats or foxes. It made the clone wonder if what was before him human or not.

He wanted to say the other was male but wasn't so sure due to the fact the other's body was covered with restraints making it impossible to tell the gender of his new roommate. The only visible part was the head of the stranger, and that was only from the beginning of the chin. He knew males had Adam's apples but without the neck the clone wasn't how else he could tell the gender differences between females and males. The genomorphs focus his education more on world issues, computer programming, and the likes more than common everyday facts, something he wished was different.

The other was also studying him, and after a while it opened it's mouth. "Can you even understand me?"

Now here Project Kr felt his face tighten, as he refused to answer. He hated when he was talked down to like that, but he tried his best to hide his thoughts as best he could. Even if he was a clone with false memories he could understand dammit! Why couldn't someone _understand_ that if they were so smart?!

His hands twitch with the eager to punch the blonde right in the middle of the eyes, a small part of him building up rage to get the job done. What he wouldn't give to punch something and break it beyond repair most preferably the other or a scientist. A small part of him wanted to ripped everything around apart, and scream till his throat was hoarse. Another part of him wondered where all the aggression had come from, it was the first time he reacted this violently to the something so small and if he had been in the right mindset, he would have worried about the blood thirsty mist clouding his mind. But right now wasn't that time. Right now he just wanted to beat that stupid smirk off the tan face.

He almost gave in to the anger had it not been for what the blond prisoner did next.

The other threw its head back as far as the restraints allowed letting out a deep throat laugh

"Sheesh Kid. I didn't mean it like that! I meant of you understood English since when I first woke up here I only spoke Japanese! But man, you should have seen the look on your face! If looks could kill, I'll be a dead man in less than a minute!" The last part of the sentence was lost in fits of chuckles as the whiskered face tried to control his laughter.

Huh? Socked Project Kr watched the other give up the battle and laughed until tears leaked out of its eyes. The other didn't stop until the need for air became necessary. It took a while for the other to calm down though and in that time Project Kr's mind focus on something the other said. A dead man? So the other was male? Good to know.

"I haven't laughed like that in months! I like you kid!" The blond said a wide smile stretching his checks. "I'm glad your funny, it makes this a little better to be stuck here. Oh by the way, my name is Naruto Uzumsaki Namikaze! I'm a male! I like ramen, my precious people, peace, leafs and foxes! I don't like the three minutes you have to wait for ramen, people who belittle others, war, someone telling me to stop talking to myself and someone trying to hurt my precious people! My hobbies include comparing ramen flavors, pranks, speaking to the guy in my head, gardening and sparring! My dream is to one day escape from Cadmus and find a home! It's nice to meet you!"

Project Kr felt himself blink as Naruto drew in a large breath after his long introduction. He finally understood the situation and he had to bite back a groan when it clicked in his head. The blond man was crazy it seems. And he was a project too. Which means Nartuto Uzumaki Namikaze was now his roommate for the unforeseen future.

Great.


	2. Chapter 2

Over time, Project Kr got used to his new roommate.

Naruto wasn't very talkative whenever the doctors were around. He gave plenty of facial expressions but he never let a sound leave his lips whenever they tried an experiment on him. No words, no screams, not even whimpers, and at times he wouldn't even blink. (he concluded this by the many complaints the scientists voiced throughout the day) Sometimes when they moved the shock levels past sixteen then the blond would grind his teeth but that would be all. The clone was, in all honesty, sometimes in awe at the fact, as the scientist grew more and more frustrated by the lack of response.

Naruto was dubbed as Project Revolution or for short Project R as his biological makeup had traces of alien energy that could apparently turn into weapons of an elemental kind. Or so the scientists believed. They didn't talk about where Naruto came from so Project Kr wasn't sure if Project R was lab made or not but he did know that they wanted whatever he held in him.

They just couldn't get to it.

It seemed nothing they did could draw out the unexplained energy force they could detect inside the other. And the blue eyed male seemed to glow from that fact as his smirk grew smugger and smugger at each attempt. The Cadmus scientists wouldn't be so easily defeated however and they grew more and more restless to get it right.

They divided their attention between the two which also drove off the heat from the clone and for that he was grateful. He guessed it was due to the fact they needed him to "grow" and though they did measure his body movements and development there was nothing that could be done until he was fully mature. He wasn't sure what that meant completely yet but he stayed in his "slumber" for longer periods of time so Project Kr counted that as a win.

Naruto on the another hand was in "full development".

The scientists were both fascinated and frustrated with this fact. Each day they tried something new, something different, and yet they never stood too close to the pod. Turns out that whatever Naruto was, he was dangerous. So much so that new recruits had to be constantly reminded by the seniors to not pass the safety line which was taped a good foot around the blond.

Project Kr, often heard them move back and forth from his pod and the other's yet the steps sound less sure, less safe whenever they were assigned to his roommate. It made him wonder why the clone didn't think Naruto was by any means threatening. Yet the scientists feared him, in their own quiet way.

He sometimes was tempted to open his eyes to see what they really did but knew not to. He didn't want to give away his slumber for what it really was.

At night- or what he thought was night. Project Kr understood the concept of time but he couldn't keep track of it, not when he never needed to- Naruto came to life. He seemed to enjoy talking the clone's ear off. He spoke of many things- his ninja training, his many colorful friends, the hobbies he used to do, the flavor of his favorite foods, - and he seemed to be convinced that he actually lived those moments. Actually believed he was Naruto Uzumaki Namikaze. The other also refused to be called Project R and demanded that the superman clone used his name.

He almost seemed normal.

But the genomorphs on top of his pod were force feeding him images just like Project Kr, so those memories were lies. They weren't real. The training he had were downloaded software, the colorful friends were programmed droids, the hobbies were just guiding books planted in his head and he had probably never even had food before just like the superman clone.

Nothing Naruto believed he experienced was real. The other experiment didn't seem to understand that, not even when the scientist mocks him about it. Not even when Kr lashed out at him some nights, where his body ached from the pain of the experiments he went through during the day. The blond would just hum, then start talking to "Kurama" once he realized that once again Project Kr would not verbally continue the conversations.

Naruto claimed that Kurama was a giant nine tailed fox which was sealed within him the day he was born. At first, they hadn't been very friendly with each other but after the Fourth Shinobi War, the two were now brothers. He said all this with a wide cheerful smile, his laugh lines pulling around his eyes so easily.

Sometimes, Kr felt bad for the other. Not only was he tortured daily but he was out of his mind as well, so far in fact that he created a voice in his head.

Other times he hated how persistent he was. Naruto took it upon himself to make the clone his friend. He would at times teach him bits and pieces of Japanese's- "Kakashi means scarecrow! He was my teacher, you know? Good old one eye Scarecrow" - and it was interesting to learn he wouldn't lie. The only language imprinted into his head was English so sometimes it felt like school to him.

Naruto would try telling jokes, each starting out with "a ninja did this one time" and for some reason, they would lead to a hilarious story about Naruto's so called old friends. Project Kr's favorites were of "Bushy Brow" but he would never admit it.

The thing though that really got to the clone were Naruto's attempts of _naming_ him of all things. "Everyone has a name. Not something that they are, but something that they are called. Kurama is the Kyuubi back home but I would never call him that after learning his name kid. You need a name. So how about... Isamu?"

"Ken?"

"Ryuunosyke?"

"Kiyoshi?"

"Takeshi?"

"Kou?

Each new night the other had a new name for him to try out but since Project Kr never said full out yes to any of them the blond would hum as if though he understood that the clone did not like them and proclaim "Ok I'll get a better one for you tomorrow and you'll love it, believe it!" The clone hated the

The clone hated the warmth that burned in his chest at each one. He felt weak and stupid for wanting one so badly and sometimes he wondered what those names meant. Naruto had been clear on saying it was a tradition back home to have a special meaning in names- it was in memory of someone else that had fallen out in the field or a way to have good luck upon the child.- he often times heard the blond mumbled about that name not fitting him.

That the kid needed a name to show how strong or amazing he really was. Then he would screw his face up like he bite into a lemon and growls something in Japanese to Kurama. Project Kr noticed that the blond tended to switch between languages often and he wondered if the ones said in English were meant for him to hear or not.

The clone grew used to it, though and would ignore the other to fall back into his dreams. He refused to admit to dreaming of the place Naruto spoke so fondly and wishful of. A place surrounded by trees, ninjas jumping upon the roofs and five stones faces watching over the village. It sounded like nothing the genomorphs could show him and he liked that. It was almost like he could live there too.

He imaged himself walking along dirt roads, looking for a ramen shop Naruto spoke so often about. He paused as a shadow flew past him and Jr...or maybe Isamu...lifted his head to look up. He would be left breathless by the ninjas that ran to and fro among the roofs for a few seconds then shrug his shoulders cause he was used to seeing them. Then he would continue on his way. His raven locks would bounce with each step as his best friend Bushy Brow complete about the latest homework assignment they had. The guy would go off again and again of how much he hated algebra like Isamu and-

"There are three intruders in the base." Naruto's voice sliced through his dream like a hot blade through butter. It was so sudden that the clone was a bit disorientated. He turned confused eyes to his roommate half annoyed for the random outburst and half curious to see what Kurama was saying this time.

He wasn't expecting to find what he did.

For once Naruto didn't look friendly. Project Kr was stunned by the serious deadly stare the blond was throwing at the door. The blue eyes were cold, in a way that made them almost seemed to be glowing in a demonic matter. His mouth was set in of a frown with the corners of his lips pulled almost into a snare. It was kind of terrifying to see and he finally learned why the scientists were scared to go near him.

Despite all the restraints, despite the fact he was only a head, despite the fact he was podded, Naruto looked every bit his true name. Project R, the _weapon,_ was prepared to kill. The clone could feel the cold preparation all the way from his pod and the promise of a battle roaring around the air of the other. This he knew, was the mysterious power Cadmus wanted.

This was the experiment they spent months on before they placed Project R into his room. This was the true nature of his roommate, _a living weapon._ Kr almost forgot to think of him as such because of how the other acted. It felt like he had been slapped back into reality, force to see what the other really was.

" Intruders?" The clone asked a slight hoarse tone in his voice. He hadn't spoken in weeks and using his voice felt odd but he didn't care about it. Not now. This was serious. If what the other said was true then their home was being attacked. He needed to prove his purpose now. He was created to fight off any attacks that came his way. "There are intruders here?"

The room lights were off like usual but he didn't miss the way the blond's nod, eyes intense at the sliding door. Kr felt slight offended that the other didn't verbally answer him but he was too busy wondering if he should trust the other. R was crazy, this he had known for the past weeks they spent together but he was also the only one who treated him like...like he mattered beyond being someone's property.

"They're coming this way," Nar- _Project R_ said. He flicked blue eyes briefly to lock with darker ones before turning them back to the door. There was shouting coming from the hallway, feet pounding on the ground and Project Kr felt his eyes widen. The other was right.

"Play dead" R ordered suddenly, eyes turning blond let his head fall down as if though he was unconscious. His super hearing picked up the slowing breath and heartbeat of the other and Project K worried his roommate really did pass out.

Before Project Kr could say or do anything to make sure the other experiment was alright the door of their room opeaned and three male teenagers clad in bright tights rushed in slamming it close behind them. The clone froze for a bit before slamming his eyes closed.

What was happening?


End file.
